#pacbio — Public Fediverse posts

🌿 Collecting samples in remote forests can mean 3–5 days before reaching the laboratory, making a continuous cold chain difficult to maintain.

100% ethanol and Allprotect preserved DNA well enough for high-quality #PacBio genome assemblies, opening new possibilities for field #genomics.

#Assembly

Pipeline release! nf-core/pacvar v1.1.0 - Neon tetra!
Longread PacBio sequencing processing for WGS and PureTarget
Please see the changelog: https://github.com/nf-core/pacvar/releases/tag/1.1.0

#alignment #longread #pacbio #puretarget #variantcalling #wgs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/ampliseq v2.18.0 - Ampliseq Version 2.18.0!
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.18.0

#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #metataxonomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/ampliseq v2.17.0 - Ampliseq Version 2.17.0!
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.17.0

#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #metataxonomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/ampliseq v2.16.1 - Ampliseq release 2.16.1 2026-01-23!
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.16.1

#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #metataxonomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/ampliseq v2.16.0 - Ampliseq Version 2.16.0!
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.16.0

#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #metataxonomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Don’t miss this spotlight talk featuring Jeremy Wilkinson from #PacBio during #PAG33, starting in one hour! 🌱🧬 Learn how HiFi long-read sequencing enables high-resolution microbiome analysis across plant, animal, and environmental systems. 🕡 6:20 PM | Pacific H-I Room

🚀 Ready to Master NGS?
Join BioResire’s 1-Month NGS Course 🧬✨

🔹 What You’ll Learn:
📖 NGS Basics
🧫 Illumina, Nanopore, PacBio platforms
🧪 Sample preparation
💻 Data analysis & genomics applications

🎯 Batch Starts: Oct 18, 2025

#BioResire #NGS #Genomics #Bioinformatics #OnlineCourse #Illumina #Nanopore #PacBio #LifeSciences #CareerGrowth #Learning

Pipeline release! nf-core/ampliseq v2.15.0 - Ampliseq Version 2.15.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.15.0

#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/ampliseq v2.14.0 - Ampliseq Version 2.14.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.14.0

#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

Probably the most complete snail genome yet, a chromosome-level assembly for the aptly-named, invasive 'Asian Tramp Snail' *Bradybaena similaris. *This particular one was not difficult - but it has been a long road to get to this point. #genomics #snails #HiFi #PacBio Link now added: https://academic.oup.com/gbe/article/17/5/evaf070/8112707

Pipeline release! nf-core/ampliseq v2.13.0 - Ampliseq Version 2.13.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.13.0

#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

I've been reviewing state of ONT & PacBio #Archaea raw data availability in public repos (preprint coming soon). It's not fantastic.

Once we upload current reads, our warehouse & partner lab might be THE top uploader in the world in terms of diversity of Archaeal species contribution.

We're also covering both #ONT and #PacBio for each species - so 2x the count.

I'll also upload all ONT raws in blow5 format as well! Down with vendor lock-in.

#microbiology #bioinformatics

Pipeline release! nf-core/pacvar v1.0.1 - v1.0.1 - Sardine [3/6/2025]!

Please see the changelog: https://github.com/nf-core/pacvar/releases/tag/1.0.1

#alignment #longread #pacbio #puretarget #variantcalling #wgs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/pacvar vv1.0.0 - nf-core/pacvarv1.0.0 - Goldfish [2/05/2024]!

Please see the changelog: https://github.com/nf-core/pacvar/releases/tag/v1.0.0

#alignment #longread #pacbio #puretarget #variantcalling #wgs #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/ampliseq v2.12.0 - Ampliseq Version 2.12.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.12.0

#16s #18s #ampliconsequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomicclassification #taxonomicprofiling #nfcore #openscience #nextflow #bioinformatics

I have a big microbial sequencing batch coming up that will require decent methylation calling.

How's ONT vs PacBio on this front? R10's direct methylation detection is exactly what I'm looking for, but curious about first-hand experience from researchers for both platforms.

#sequencing #bioinformatics #nanopore #pacbio

Pipeline release! nf-core/ampliseq v2.11.0 - Ampliseq Version 2.11.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.11.0

#16s #18s #amplicon-sequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomic-classification #taxonomic-profiling #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/ampliseq v2.10.0 - Ampliseq Version 2.10.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.10.0

#16s #18s #amplicon-sequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomic-classification #taxonomic-profiling #nfcore #openscience #nextflow #bioinformatics

Celebrating - finally - 72Gb worth of PacBio HiFi data from one of my favourite snails! At last able to begin the research proper. Of course the assembly wont be easy but at least we have the data to do it. 👏🥂🐌 #snail #PacBio #HiFi #Genomics

Pipeline release! nf-core/ampliseq v2.9.0 - Ampliseq Version 2.9.0!

Please see the changelog: https://github.com/nf-core/ampliseq/releases/tag/2.9.0

#16s #18s #amplicon-sequencing #edna #illumina #iontorrent #its #metabarcoding #metagenomics #microbiome #pacbio #qiime2 #rrna #taxonomic-classification #taxonomic-profiling #nfcore #openscience #nextflow #bioinformatics

minimap2-rs updated! Now using minimap 2.27. Needletail + rayon support! Thanks for all the pull requests to help get this here!

https://crates.io/crates/minimap2
All changes: https://github.com/jguhlin/minimap2-rs/?tab=readme-ov-file#0117-minimap2-227
#rust #bioinformatics #genomics #nanopore #pacbio #RustLang

Digging through some old #pacbio data from 2015. A quick way to handle bax files from back then seems to be bax2bam off conda - but the latest version (2 years old) has a weird bug that's never been fixed.

If you're getting read quality metrics error during conversion, try bax2bam=0.0.9 installation instead.

Not liking the idea of deprecated proprietary binary data in public (NCBI) databases :/ #bioinformatics

Announcing minimap2-rs 0.1.15 release - Biggest features are compilation on aarch64, and better support for static builds. Also reduced dependency version to remove unnecessary tokio dependencies. Thanks again to the contributors helping me with this code!

Changelog: https://github.com/jguhlin/minimap2-rs#0115-minimap2-226

Crate: https://crates.io/crates/minimap2

Sys Crate: https://crates.io/crates/minimap2-sys

#rust #nanopore #pacbio #bioinformatics #genomics